Fifteen-year-old Kafka Tamura has a bad relationship with Koichi, his sculptor father, and his mother left with his sister when he was four. The insensitive Koichi has told the boy that one day he will have sex with both his mother and sister, a prophecy tainting his desire to find them. Kafka runs away from home, and Murakami alternates his story with that of Satoru Nakata, an elderly man from the same Tokyo neighborhood. Nakata has lost his memory and the ability to read and write following a mysterious accident when he was a schoolboy in 1944. He lives on a government subsidy and the money he makes from finding lost cats, with which he can communicate much better than with humans. Nakata is an extreme example of Murakami’s patented passive protagonists. He simply accepts what life offers, enjoying its simple pleasures.

Kafka makes his way to Takamutsu on the island of Shikoku and to the Komura Memorial Library, where a wealthy man’s collection resides. He meets Oshima, a library assistant, and Miss Saeki, the library director. She was once famous for composing and singing a popular song, “Kafka on the Shore,” but retreated from the world following the death of her lover, the son of the Komura family. Kafka becomes Oshima’s assistant in exchange for room and board and finds himself visited by the spirit of the younger Miss Saeki, whom he suspects may be his mother. He also meets Sakura, a young hairdresser, and is torn between wanting to have sex with her and wanting her to be his lost sister. Kafka and Oshima discuss the Oedipal nature of his quandary.

In her review of Haruki Marakami's novel Kafka on the Shore, Laura Miller, writing for the New York Times Book Review, stated that Kafka is a departure for the popular Japanese author. More often than not, Marakami's protagonists are middle-aged men. However, in Kafka on the Shore, the main character is a fifteen-year-old runaway, Kafka Tamura. He does not get along with his father and does not know where his mother is. She disappeared with Kafka's sister when the boy was only four.

It is through Kafka's adventures that the story unwinds. However, there is a slightly connected second story that is also being told. This other story involves Satoru Nakata, now an old man. But when Satoru was a youth, he lost consciousness while on a field trip with his schoolmates. Through this experience, which is not explained, Satoru lost all his memories but gained the ability to speak to cats. This new skill allows him to find lost cats (a theme that is a strong one in Marakami's most popular novel, The Wind-Up Bird Chronicle).

John Updike, in his review for the New Yorker, called Marakami's novel "a real page-turner, as well as an insistently metaphysical mind-bender." Updike was referring to the dream-like character of Marakami's writing. The major plotline is definitely dreamlike. The young teen boy, Kafka, and the old man, Satoru, separately are in search of a mysterious entrance to a special, spiritual land. Through their adventures, they encounter murders, a group of soldiers who have not aged since the end of World War II, and weird rainstorms that at times produce falling fish. These two characters, though their lives are entwined, never meet. There are hints that Kafka and Satoru are different versions of the same person. Sakura, a young woman Kafka meets on the bus as he is running away, may also be Kafka's missing sister. And the cat-killing Johnnie Walker could well be a disguised version of Kafka's father. Miss Saeki, the manager of the library where Kafka spends most of his time after he runs away, may be the young boy's mother.

Marakami has explained that the book contains several riddles that will become apparent only after the novel is reread several times.